Plant genomics · Bioinformatics consulting

Your lab's genomics, handled end to end.

From raw reads to publication figures: assembly, annotation, transcriptomics, methylation, and metabarcoding for plant and pathogen systems. One specialist, accountable for the whole analysis.

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7 PUBLICATIONS · UNIVERSITY RESEARCH COLLABORATIONS · PYTHON / R / HPC

analysis_console

COV

REF

5mC

coverage · reference · methylation●

Services · Directory

Everything I do, in one place.

Full service details

01Genome assembly & polishing reviewAssemble or rescue, then polish to reference quality.QC reportpolished assembly 02Genome annotationEvidence-based structural gene models.GFF3tracks 03Functional annotationWhat genes do: GO, pathways, gene families.GO / KEGGgene sets 04Repeat annotationTransposable-element and repeat landscape.TE librarymasked 05Comparative genomicsOrthology, synteny, gene-family evolution.treesdotplots 06RNA-seq & transcriptomicsDifferential expression and dual RNA-seq.DE tablesfigures 07DNA methylation & modified basesWGBS, EM-seq, and Nanopore 5mC.DMRsprofiles 08Metabarcoding & barcode benchmarkingAmplicon pipelines and marker benchmarking.ASVtaxonomy 09Custom bioinformatics pipelinesReproducible, documented, re-runnable.Snakemake / Nextflow 10Manuscript-ready figures & methodsFigures, methods, and reproducible code.figuresmethods

How the pipeline flows

Raw reads in. Publishable results out.

Raw reads

Illumina · PacBio · Nanopore

Assembly

contiguous, polished

Annotation

structural + functional

Analysis

expression · methylation

Interpretation

candidate genes, biology

Manuscript

figures, methods, code

Academic-standard analysis

Methods chosen for your biology and defensible to reviewers.

Results, not just scripts

Interpreted findings, figures, and documented methods.

A specialist's eye

Plant genomes, oomycetes, and plant-microbe interactions.

Led by

Pablo Vargas Mejía

Plant genomics and bioinformatics researcher specializing in molecular plant pathology. Doctoral research at UNAM on the epigenomics of Phytophthora capsici, with university research collaborations in plant pathology and genomics.

About me

Have a dataset that needs expert hands?

Tell me about your organism, your data, and your timeline. I'll reply with whether I can help and how we would scope it. No obligation.

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